6WXH

Colicin E1 fragment in nanodisc-embedded TolC


Experimental Data Snapshot

  • Method: ELECTRON MICROSCOPY
  • Resolution: 3.09 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 

Starting Model: experimental
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wwPDB Validation   3D Report Full Report


This is version 1.2 of the entry. See complete history


Literature

Colicin E1 opens its hinge to plug TolC.

Budiardjo, S.J.Stevens, J.J.Calkins, A.L.Ikujuni, A.P.Wimalasena, V.K.Firlar, E.Case, D.A.Biteen, J.S.Kaelber, J.T.Slusky, J.S.G.

(2022) Elife 11

  • DOI: https://doi.org/10.7554/eLife.73297
  • Primary Citation of Related Structures:  
    6WXH, 6WXI

  • PubMed Abstract: 

    The double membrane architecture of Gram-negative bacteria forms a barrier that is impermeable to most extracellular threats. Bacteriocin proteins evolved to exploit the accessible, surface-exposed proteins embedded in the outer membrane to deliver cytotoxic cargo. Colicin E1 is a bacteriocin produced by, and lethal to, Escherichia coli that hijacks the outer membrane proteins (OMPs) TolC and BtuB to enter the cell. Here, we capture the colicin E1 translocation domain inside its membrane receptor, TolC, by high-resolution cryo-electron microscopy to obtain the first reported structure of a bacteriocin bound to TolC. Colicin E1 binds stably to TolC as an open hinge through the TolC pore-an architectural rearrangement from colicin E1's unbound conformation. This binding is stable in live E. coli cells as indicated by single-molecule fluorescence microscopy. Finally, colicin E1 fragments binding to TolC plug the channel, inhibiting its native efflux function as an antibiotic efflux pump, and heightening susceptibility to three antibiotic classes. In addition to demonstrating that these protein fragments are useful starting points for developing novel antibiotic potentiators, this method could be expanded to other colicins to inhibit other OMP functions.


  • Organizational Affiliation

    Center for Computational Biology, The University of Kansas, Lawrence, United States.


Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Outer membrane protein TolC
A, B, C
493Escherichia coli K-12Mutation(s): 0 
Gene Names: tolCcolE1-imtcBmukArefItocweeAb3035JW5503
Membrane Entity: Yes 
UniProt
Find proteins for P02930 (Escherichia coli (strain K12))
Explore P02930 
Go to UniProtKB:  P02930
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP02930
Sequence Annotations
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  • Reference Sequence
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 2
MoleculeChains Sequence LengthOrganismDetailsImage
Colicin-E1198Escherichia coliMutation(s): 0 
Gene Names: cea
Membrane Entity: Yes 
UniProt
Find proteins for P02978 (Escherichia coli)
Explore P02978 
Go to UniProtKB:  P02978
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP02978
Sequence Annotations
Expand
  • Reference Sequence
Experimental Data & Validation

Experimental Data

  • Method: ELECTRON MICROSCOPY
  • Resolution: 3.09 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 
EM Software:
TaskSoftware PackageVersion
RECONSTRUCTIONcryoSPARC2.14.2
MODEL REFINEMENTPHENIX1.14-3260
MODEL REFINEMENTCoot0.8.9.2-pre
MODEL REFINEMENTISOLDE1.0b4.dev1
MODEL REFINEMENTAmber20

Structure Validation

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Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)United StatesDP2GM128201
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)United StatesP20GM113117
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)United StatesP20GM103638

Revision History  (Full details and data files)

  • Version 1.0: 2021-05-12
    Type: Initial release
  • Version 1.1: 2022-05-04
    Changes: Database references
  • Version 1.2: 2024-05-15
    Changes: Data collection, Refinement description